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Atomic-resolution structure of the yeast Sla1 SH3 domain 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z9Z PDB ENTRY 1Z9Z
Crystallization Crystal Properties Matthews coefficient Solvent content 1.67 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.94 α = 90 b = 55.25 β = 90 c = 85.29 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A EMBL/DESY, HAMBURG BW7A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.2 20 100 0.04 19.4 5.9 33200 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 100 0.53 2.8 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1Z9Z 1.2 10 33200 1747 100 0.151 0.148 0.1603 0.188 0.199 RANDOM 13.21
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.29 1.65 -1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.924 r_dihedral_angle_4_deg 23.842 r_dihedral_angle_3_deg 10.963 r_scangle_it 7.4 r_dihedral_angle_1_deg 6.301 r_scbond_it 5.705 r_mcangle_it 4.09 r_mcbond_it 2.99 r_angle_refined_deg 1.949 r_angle_other_deg 0.985
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.924 r_dihedral_angle_4_deg 23.842 r_dihedral_angle_3_deg 10.963 r_scangle_it 7.4 r_dihedral_angle_1_deg 6.301 r_scbond_it 5.705 r_mcangle_it 4.09 r_mcbond_it 2.99 r_angle_refined_deg 1.949 r_angle_other_deg 0.985 r_xyhbond_nbd_refined 0.275 r_symmetry_hbond_refined 0.27 r_nbd_refined 0.259 r_symmetry_vdw_other 0.222 r_nbd_other 0.202 r_symmetry_vdw_refined 0.198 r_nbtor_refined 0.18 r_chiral_restr 0.126 r_nbtor_other 0.094 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 940 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing